Allegations the regime used chemical weapons have not triggered a strong response despite Barack Obama's claim it would be a "red line". Photo / AP

Shia residents of Damascus have described how armed Sunni militiamen daubed crosses on the doors of homes and assassinated religious leaders in the street.

The testimonies given by Shia refugees who have fled to Lebanon paint a graphic picture of how the Syrian rebellion has descended into deep-seated sectarianism, with hardline Sunni rebels bent on targeting minorities and building an uncompromising Islamic state.

"I heard the imam in the mosque next to our home call for jihad against the Syrian regime, and against the Alawites and Shia. They were shouting it from the minarets," said Awatif, 60, too frightened of reprisals to give her family name.

"The neighbourhood next to ours was burned. Friends found crosses marked in red on their doors and then they were attacked. That was when we knew we had to leave."

Awatif and her elderly husband Ali, 70, are among thousands of Shia families to have sought refuge across the border in Lebanon, in their case in the mountain village of Machaghara.

In Damascus, their home was near the Sayyida Zainab shrine, believed to house the remains of the granddaughter of the Prophet Muhammad and one of the holiest sites for Shias.

At the outset of the rebellion two years ago, some tacitly supported President Bashar al-Assad, whose Alawite sect is a branch of Shia Islam; others were less keen, and blamed him for killing opponents.

But after sustained persecution by Sunni militias they say their survival depends on the protection of the Assad regime, which now funds their neighbourhood defence forces.

"We believe now that we have a religious cause as we feel that the Shia now are being targeted. Sunni gangs told us to take the Sayeda Zainab shrine and to leave," said Fatma Merhi, 77, sitting alone in a bare room in her house in Machaghara. "If the regime goes now we will have no future."

Above her is a portrait of her son Radwan Merhi, 53, who was in a Shia unit fighting in Damascus when he was shot dead by a rebel sniper.

In early 2012, the area suffered a wave of attacks by radical Sunni militiamen. It began with death threats but the violence grew to include the suicide bombings now rife across Damascus, and a self-confessed trademark of the al-Qaeda linked group Jabhat al-Nusra.

On April 13, 2012, two gunmen assassinated Sayed Naser al-Alawi, a Shia religious scholar and prayer leader in the Husseiniyah mosque, close to the Sayyida Zainab shrine.

Ali's son, who gave his name as Abu Haider, 29, was a caretaker in the mosque. He said: "I started receiving death threats. I found letters stuck to the gates outside the mosque. They used my family name and called me a 'Shia dog'.

"The third letter gave me 72 hours to leave. It said they would cut my head off and leave it hanging on the Sayyida Zainab shrine."

Three days later a group of masked armed gunmen mistakenly kidnapped a man in a cafeteria when Abu Haider believed he was the target.